Grab lab file using command line:
# Step 1
cd ~/Documents
mkdir lab11
cd lab11
# Step 2
wget https://raw.githubusercontent.com/USCbiostats/PM566/master/website/content/assignment/11-lab.Rmd
And remember to set eval=TRUE
plot_ly() and ggplotly() functionsplot_geo()We will work with COVID data downloaded from the New York Times. The dataset consists of COVID-19 cases and deaths in each US state during the course of the COVID epidemic.
The objective of this lab is to explore relationships between cases, deaths, and population sizes of US states, and plot data to demonstrate this
## data extracted from New York Times state-level data from NYT Github repository
# https://github.com/nytimes/covid-19-data
## state-level population information from us_census_data available on GitHub repository:
# https://github.com/COVID19Tracking/associated-data/tree/master/us_census_data
# load COVID state-level data from NYT
cv_states <- as.data.frame(data.table::fread("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv"))
# load state population data
state_pops <- as.data.frame(data.table::fread("https://raw.githubusercontent.com/COVID19Tracking/associated-data/master/us_census_data/us_census_2018_population_estimates_states.csv"))
state_pops$abb <- state_pops$state
state_pops$state <- state_pops$state_name
state_pops$state_name <- NULL
cv_states <- merge(cv_states, state_pops, by = 'state')
head, and tail of
the datadim(cv_states)
## [1] 51074 9
head(cv_states)
## state date fips cases deaths geo_id population pop_density abb
## 1 Alabama 2021-07-15 1 557578 11439 1 4887871 96.50939 AL
## 2 Alabama 2021-07-28 1 577463 11510 1 4887871 96.50939 AL
## 3 Alabama 2021-08-27 1 681828 12153 1 4887871 96.50939 AL
## 4 Alabama 2021-06-08 1 546540 11220 1 4887871 96.50939 AL
## 5 Alabama 2022-03-17 1 1290692 18998 1 4887871 96.50939 AL
## 6 Alabama 2021-07-30 1 580193 11516 1 4887871 96.50939 AL
tail(cv_states)
## state date fips cases deaths geo_id population pop_density abb
## 51069 Wyoming 2021-11-08 56 105990 1243 56 577737 5.950611 WY
## 51070 Wyoming 2022-11-01 56 178866 1914 56 577737 5.950611 WY
## 51071 Wyoming 2021-08-15 56 68272 793 56 577737 5.950611 WY
## 51072 Wyoming 2022-11-08 56 179366 1917 56 577737 5.950611 WY
## 51073 Wyoming 2022-02-16 56 153663 1689 56 577737 5.950611 WY
## 51074 Wyoming 2022-01-20 56 133495 1601 56 577737 5.950611 WY
str(cv_states)
## 'data.frame': 51074 obs. of 9 variables:
## $ state : chr "Alabama" "Alabama" "Alabama" "Alabama" ...
## $ date : IDate, format: "2021-07-15" "2021-07-28" ...
## $ fips : int 1 1 1 1 1 1 1 1 1 1 ...
## $ cases : int 557578 577463 681828 546540 1290692 580193 551298 1531305 546845 1479605 ...
## $ deaths : int 11439 11510 12153 11220 18998 11516 11358 20533 11249 20048 ...
## $ geo_id : int 1 1 1 1 1 1 1 1 1 1 ...
## $ population : int 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 ...
## $ pop_density: num 96.5 96.5 96.5 96.5 96.5 ...
## $ abb : chr "AL" "AL" "AL" "AL" ...
# format the date
cv_states$date <- as.Date(cv_states$date, format="%Y-%m-%d")
# format the state and state abbreviation (abb) variables
state_list <- unique(cv_states$state)
cv_states$state <- factor(cv_states$state, levels = state_list)
abb_list <- unique(cv_states$abb)
cv_states$abb <- factor(cv_states$abb, levels = abb_list)
### FINISH THE CODE HERE
# order the data first by state, second by date
cv_states <- cv_states[order(cv_states$state, cv_states$date), ]
# Confirm the variables are now correctly formatted
str(cv_states)
## 'data.frame': 51074 obs. of 9 variables:
## $ state : Factor w/ 52 levels "Alabama","Alaska",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ date : Date, format: "2020-03-13" "2020-03-14" ...
## $ fips : int 1 1 1 1 1 1 1 1 1 1 ...
## $ cases : int 6 12 23 29 39 51 78 106 131 157 ...
## $ deaths : int 0 0 0 0 0 0 0 0 0 0 ...
## $ geo_id : int 1 1 1 1 1 1 1 1 1 1 ...
## $ population : int 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 ...
## $ pop_density: num 96.5 96.5 96.5 96.5 96.5 ...
## $ abb : Factor w/ 52 levels "AL","AK","AZ",..: 1 1 1 1 1 1 1 1 1 1 ...
head(cv_states)
## state date fips cases deaths geo_id population pop_density abb
## 871 Alabama 2020-03-13 1 6 0 1 4887871 96.50939 AL
## 676 Alabama 2020-03-14 1 12 0 1 4887871 96.50939 AL
## 928 Alabama 2020-03-15 1 23 0 1 4887871 96.50939 AL
## 417 Alabama 2020-03-16 1 29 0 1 4887871 96.50939 AL
## 714 Alabama 2020-03-17 1 39 0 1 4887871 96.50939 AL
## 167 Alabama 2020-03-18 1 51 0 1 4887871 96.50939 AL
tail(cv_states)
## state date fips cases deaths geo_id population pop_density abb
## 50232 Wyoming 2022-11-03 56 178866 1914 56 577737 5.950611 WY
## 50842 Wyoming 2022-11-04 56 178866 1914 56 577737 5.950611 WY
## 50409 Wyoming 2022-11-05 56 178866 1914 56 577737 5.950611 WY
## 50830 Wyoming 2022-11-06 56 178866 1914 56 577737 5.950611 WY
## 50524 Wyoming 2022-11-07 56 178866 1914 56 577737 5.950611 WY
## 51072 Wyoming 2022-11-08 56 179366 1917 56 577737 5.950611 WY
# Inspect the range values for each variable. What is the date range? The range of cases and deaths?
head(cv_states)
## state date fips cases deaths geo_id population pop_density abb
## 871 Alabama 2020-03-13 1 6 0 1 4887871 96.50939 AL
## 676 Alabama 2020-03-14 1 12 0 1 4887871 96.50939 AL
## 928 Alabama 2020-03-15 1 23 0 1 4887871 96.50939 AL
## 417 Alabama 2020-03-16 1 29 0 1 4887871 96.50939 AL
## 714 Alabama 2020-03-17 1 39 0 1 4887871 96.50939 AL
## 167 Alabama 2020-03-18 1 51 0 1 4887871 96.50939 AL
summary(cv_states)
## state date fips cases
## Washington : 1023 Min. :2020-01-21 Min. : 1.00 Min. : 1
## Illinois : 1020 1st Qu.:2020-11-02 1st Qu.:16.00 1st Qu.: 88644
## California : 1019 Median :2021-07-05 Median :29.00 Median : 341318
## Arizona : 1018 Mean :2021-07-05 Mean :29.78 Mean : 811407
## Massachusetts: 1012 3rd Qu.:2022-03-08 3rd Qu.:44.00 3rd Qu.: 954938
## Wisconsin : 1008 Max. :2022-11-08 Max. :72.00 Max. :11390274
## (Other) :44974
## deaths geo_id population pop_density
## Min. : 0 Min. : 1.00 Min. : 577737 Min. : 1.292
## 1st Qu.: 1364 1st Qu.:16.00 1st Qu.: 1805832 1st Qu.: 43.659
## Median : 5104 Median :29.00 Median : 4468402 Median : 107.860
## Mean :11352 Mean :29.78 Mean : 6404128 Mean : 422.942
## 3rd Qu.:14375 3rd Qu.:44.00 3rd Qu.: 7535591 3rd Qu.: 229.511
## Max. :97064 Max. :72.00 Max. :39557045 Max. :11490.120
## NA's :971
## abb
## WA : 1023
## IL : 1020
## CA : 1019
## AZ : 1018
## MA : 1012
## WI : 1008
## (Other):44974
min(cv_states$date)
## [1] "2020-01-21"
max(cv_states$date)
## [1] "2022-11-08"
new_cases and new_deaths and
correct outliersAdd variables for new cases, new_cases, and new
deaths, new_deaths:
new_cases equal to the difference
between cases on date i and date i-1, starting on date i=2Filter to dates after June 1, 2021
Use plotly for EDA: See if there are outliers or
values that don’t make sense for new_cases and
new_deaths. Which states and which dates have strange
values?
Correct outliers: Set negative values for new_cases
or new_deaths to 0
Recalculate cases and deaths as
cumulative sum of updated new_cases and
new_deaths
Get the rolling average of new cases and new deaths to smooth over time
Inspect data again interactively
# Add variables for new_cases and new_deaths by state:
for (i in 1:length(state_list)) {
cv_subset = subset(cv_states, state == state_list[i])
cv_subset = cv_subset[order(cv_subset$date),]
# add starting level for new cases and deaths
cv_subset$new_cases = cv_subset$cases[1]
cv_subset$new_deaths = cv_subset$deaths[1]
for (j in 2:nrow(cv_subset)) {
cv_subset$new_cases[j] = cv_subset$cases[j] - cv_subset$cases[j-1]
cv_subset$new_deaths[j] = cv_subset$deaths[j] - cv_subset$deaths[j-1]
}
# include in main dataset
cv_states$new_cases[cv_states$state==state_list[i]] = cv_subset$new_cases
cv_states$new_deaths[cv_states$state==state_list[i]] = cv_subset$new_deaths
}
# Focus on recent dates
cv_states <- cv_states %>% dplyr::filter(date >= "2021-06-01")
### FINISH THE CODE HERE
# Inspect outliers in new_cases using plotly
p1<-ggplot(cv_states, aes(x = date, y = new_cases, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p1)
p1<-NULL # to clear from workspace
p2<-ggplot(cv_states, aes(x = date, y = new_deaths, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p2)
p2<-NULL # to clear from workspace
# set negative new case or death counts to 0
cv_states$new_cases[cv_states$new_cases<0] = 0
cv_states$new_deaths[cv_states$new_deaths<0] = 0
# Recalculate `cases` and `deaths` as cumulative sum of updated `new_cases` and `new_deaths`
for (i in 1:length(state_list)) {
cv_subset = subset(cv_states, state == state_list[i])
# add starting level for new cases and deaths
cv_subset$cases = cv_subset$cases[1]
cv_subset$deaths = cv_subset$deaths[1]
for (j in 2:nrow(cv_subset)) {
cv_subset$cases[j] = cv_subset$new_cases[j] + cv_subset$cases[j-1]
cv_subset$deaths[j] = cv_subset$new_deaths[j] + cv_subset$deaths[j-1]
}
# include in main dataset
cv_states$cases[cv_states$state==state_list[i]] = cv_subset$cases
cv_states$deaths[cv_states$state==state_list[i]] = cv_subset$deaths
}
# Smooth new counts
cv_states$new_cases = zoo::rollmean(cv_states$new_cases, k=7, fill=NA, align='right') %>% round(digits = 0)
cv_states$new_deaths = zoo::rollmean(cv_states$new_deaths, k=7, fill=NA, align='right') %>% round(digits = 0)
# Inspect data again interactively
p2<-ggplot(cv_states, aes(x = date, y = new_deaths, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p2)
#p2=NULL
Add population-normalized (by 100,000) variables for each
variable type (rounded to 1 decimal place). Make sure the variables you
calculate are in the correct format (numeric). You can use
the following variable names:
per100k = cases per 100,000 populationnewper100k= new cases per 100,000deathsper100k = deaths per 100,000newdeathsper100k = new deaths per 100,000Add a “naive CFR” variable representing
deaths / cases on each date for each state
Create a dataframe representing values on the most recent date,
cv_states_today, as done in lecture
# add population normalized (by 100,000) counts for each variable
cv_states$per100k = as.numeric(format(round(cv_states$cases/(cv_states$population/100000),1),nsmall=1))
cv_states$newper100k = as.numeric(format(round(cv_states$new_cases/(cv_states$population/100000),1),nsmall=1))
cv_states$deathsper100k = as.numeric(format(round(cv_states$deaths/(cv_states$population/100000),1),nsmall=1))
cv_states$newdeathsper100k = as.numeric(format(round(cv_states$new_deaths/(cv_states$population/100000),1),nsmall=1))
# add a naive_CFR variable = deaths / cases
cv_states = cv_states %>% mutate(naive_CFR = round((deaths*100/cases),2))
# create a `cv_states_today` variable
cv_states_today = subset(cv_states, date==max(cv_states$date))
plot_ly()plot_ly() representing
pop_density vs. various variables (e.g. cases,
per100k, deaths, deathsper100k)
for each state on most recent date (cv_states_today)
hovermode = "compare"# pop_density vs. cases
cv_states_today %>%
plot_ly(x = ~pop_density, y = ~cases,
type = 'scatter', mode = 'markers', color = ~state,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))
# filter out "District of Columbia"
cv_states_today_filter <- cv_states_today %>% filter(state!="District of Columbia")
# pop_density vs. cases after filtering
cv_states_today_filter %>%
plot_ly(x = ~pop_density, y = ~cases,
type = 'scatter', mode = 'markers', color = ~state,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))
# pop_density vs. deathsper100k
cv_states_today_filter %>%
plot_ly(x = ~pop_density, y = ~deathsper100k,
type = 'scatter', mode = 'markers', color = ~state,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))
# Adding hoverinfo
cv_states_today_filter %>%
plot_ly(x = ~pop_density, y = ~deathsper100k,
type = 'scatter', mode = 'markers', color = ~state,
size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5),
hoverinfo = 'text',
text = ~paste( paste(state, ":", sep=""), paste(" Cases per 100k: ", per100k, sep="") ,
paste(" Deaths per 100k: ", deathsper100k, sep=""), sep = "<br>")) %>%
layout(title = "Population-normalized COVID-19 deaths (per 100k) vs. population density for US states",
yaxis = list(title = "Deaths per 100k"), xaxis = list(title = "Population Density"),
hovermode = "compare")
ggplotly() and geom_smooth()pop_density vs. newdeathsper100k
create a chart with the same variables using
gglot_ly()geom_smooth()
pop_density is a
correlate of newdeathsper100k?p <- ggplot(cv_states_today_filter, aes(x=pop_density, y=deathsper100k, size=population)) + geom_point() + geom_smooth()
ggplotly(p)
naive_CFR for all states
over time using plot_ly()
naive_CFR for
the states that had an increase in September. How have they changed over
time?new_cases and new_deaths together in one plot.
Hint: use add_layer()
# Line chart for naive_CFR for all states over time using `plot_ly()`
plot_ly(cv_states, x = ~date, y = ~naive_CFR, color = ~state, type = "scatter", mode = "lines")
# Line chart for Florida showing new_cases and new_deaths together
cv_states %>% filter(state=="Florida") %>% plot_ly(x = ~date, y = ~new_cases, type = "scatter", mode = "lines") %>% add_lines(x = ~date, y = ~new_deaths, type = "scatter", mode = "lines")
Create a heatmap to visualize new_cases for each state
on each date greater than June 1st, 2021 - Start by mapping selected
features in the dataframe into a matrix using the tidyr
package function pivot_wider(), naming the rows and
columns, as done in the lecture notes - Use plot_ly() to
create a heatmap out of this matrix. Which states stand out? - Repeat
with newper100k variable. Now which states stand out? -
Create a second heatmap in which the pattern of new_cases
for each state over time becomes more clear by filtering to only look at
dates every two weeks
# Map state, date, and new_cases to a matrix
library(tidyr)
cv_states_mat <- cv_states %>% select(state, date, new_cases) %>% dplyr::filter(date>as.Date("2022-06-15"))
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = new_cases))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)
# Create a heatmap using plot_ly()
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
z=~cv_states_mat2,
type="heatmap",
showscale=T)
# Repeat with newper100k
cv_states_mat <- cv_states %>% select(state, date, newper100k) %>% dplyr::filter(date>as.Date("2021-06-15"))
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = ________))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
z=~cv_states_mat2,
type="heatmap",
showscale=T)
# Create a second heatmap after filtering to only include dates every other week
filter_dates <- seq(as.Date("2021-06-15"), as.Date("2021-11-01"), by=________)
cv_states_mat <- cv_states %>% select(state, date, newper100k) %>% filter(date %in% filter_dates)
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = ________))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)
# Create a heatmap using plot_ly()
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
z=~cv_states_mat2,
type="heatmap",
showscale=T)
naive_CFR by state on
October 15, 2021naive_CFR by state
on most recent datesubplot(). Make sure
the shading is for the same range of values (google is your friend for
this)### For specified date
pick.date = "2021-10-15"
# Extract the data for each state by its abbreviation
cv_per100 <- cv_states %>% filter(date==pick.date) %>% select(state, abb, newper100k, cases, deaths) # select data
cv_per100$state_name <- cv_per100$state
cv_per100$state <- cv_per100$abb
cv_per100$abb <- NULL
# Create hover text
cv_per100$hover <- with(cv_per100, paste(state_name, '<br>', "Cases per 100k: ", newper100k, '<br>', "Cases: ", cases, '<br>', "Deaths: ", deaths))
# Set up mapping details
set_map_details <- list(
scope = 'usa',
projection = list(type = 'albers usa'),
showlakes = TRUE,
lakecolor = toRGB('white')
)
# Make sure both maps are on the same color scale
shadeLimit <- 125
# Create the map
fig <- plot_geo(cv_per100, locationmode = 'USA-states') %>%
add_trace(
z = ~newper100k, text = ~hover, locations = ~state,
color = ~newper100k, colors = 'Purples'
)
fig <- fig %>% colorbar(title = paste0("Cases per 100k: ", pick.date), limits = c(0,shadeLimit))
fig <- fig %>% layout(
title = paste('Cases per 100k by State as of ', pick.date, '<br>(Hover for value)'),
geo = set_map_details
)
fig_pick.date <- fig
#############
### Map for today's date
# Extract the data for each state by its abbreviation
cv_per100 <- cv_states_today %>% select(state, abb, newper100k, cases, deaths) # select data
cv_per100$state_name <- cv_per100$state
cv_per100$state <- cv_per100$abb
cv_per100$abb <- NULL
# Create hover text
cv_per100$hover <- with(cv_per100, paste(state_name, '<br>', "Cases per 100k: ", newper100k, '<br>', "Cases: ", cases, '<br>', "Deaths: ", deaths))
# Set up mapping details
set_map_details <- list(
scope = 'usa',
projection = list(type = 'albers usa'),
showlakes = TRUE,
lakecolor = toRGB('white')
)
# Create the map
fig <- plot_geo(cv_per100, locationmode = 'USA-states') %>%
add_trace(
z = ~newper100k, text = ~hover, locations = ~state,
color = ~newper100k, colors = 'Purples'
)
fig <- fig %>% colorbar(title = paste0("Cases per 100k: ", Sys.Date()), limits = c(0,shadeLimit))
fig <- fig %>% layout(
title = paste('Cases per 100k by State as of', Sys.Date(), '<br>(Hover for value)'),
geo = set_map_details
)
fig_Today <- fig
### Plot together
________(fig_pick.date, fig_Today, nrows = 2, margin = .05)